- Angst? What Angst?: In Twilight's final journal entry, where she writes about defeating Tirek and receiving a "beautiful, sparkly and colorful castle," she doesn't mention anything about the destruction of her old library, or the uncomfortableness she would show the following season.
- Fanfic Fuel: While the backstory of Equestria Josses a lot of popular fan theories, there is still plenty of breeding ground for new ones — the backstory of Princess Amore, the original ruler of the Crystal Empire, Star Swirl developing more sophisticated time travel spells that it's implied he used to visit the future, the idea of the pegasi and the griffons being involved in a war prior to Equestria's founding, a major battle between the Manticores and Zebras and Luna and Celestia making it clear there are other alicorns out there that they used to live with but not going into any detail on the matter. Not to mention whatever adventures Luna and Celestia had before they became princesses, as both sisters were already full-grown adults when Starswirl first approached them.
- Funny Moments: Most of Pinkie's entries, especially her discussion of the phrase "slippery when wet". Also, as mentioned in Twilight's final entry, Discord highlighted the entries of each of the Mane Cast where they got their keys... but Pinkie's "Oh my gosh, I'm an Apple!" entry is also highlighted, for no apparent reason. (Discord probably just found it hilarious)
- Tear Jerker: Reading Luna's entries just makes her eventual FaceHeel Turn even worse. Also, every time Celestia talks about how much she loves her sister, especially "My sister and I were meant to rule together." The entries also establish that Star Swirl the Bearded has seen Equestria's future. He most likely knows about Luna turning into Nightmare Moon but can't say anything about it.
YMMV / The Journal of the Two Sisters